Juvenile hormones (JHs) are key endocrine factors that regulate various physiological phenomena in crustaceans, similar to insects. In crustaceans, such as Daphnia, JHs regulate unique environmental responses, including environmental sex determination (ESD) and inducible defenses. Functional analyses of JH receptors involved in signal transduction are also underway. However, the biosynthetic organs responsible for JH production and the structural details of JH in the body remain unclear. In contrast to Daphnia, methyl farnesoate (MF) is synthesized in the mandibular organ of decapod crustaceans, such as shrimp and crabs, and is known to regulate molting and reproduction. However, research on the molecular signaling cascade of JHs in these species has made little progress. When discussing JHs in crustaceans, it is crucial to avoid lumping together the knowledge from these entirely different taxonomic groups under the umbrella of “crustaceans.” Instead, a comparative approach should be adopted, considering the phylogenetic relationships within Pancrustacea, which includes both insects and crustaceans.